u 87 mg human brain immortalized cell line  (ATCC)

Journal: Molecular Metabolism

Article Title: A targeted metabolomic method to detect epigenetically relevant metabolites

doi: 10.1016/j.molmet.2026.102342

Figure Lengend Snippet: Distribution of acetyl-CoA isotopomers following [U–13C]glucose and [U–13C]glutamine incubation with an isogenic gain-of-function mutation (R132H) in the metabolic enzyme Isocitrate Dehydrogenase 1 (IDH1). U-87 MG human brain immortalized cell line, either wild-type or harboring the IDH1-R132H mutation, was incubated with [U– 13 C]glucose or [U– 13 C]glutamine for 20 and 72 h. The x axis represents the different acetyl-CoA isotopomers, showing the number of incorporated 13C atoms, with their origins within the acetyl-CoA structure noted in parentheses (see also ). The y axis indicates the percentage abundance of each isotopomer population, with n = 5 per condition after correction for natural abundance (refer to the Methods section 4.6.3). Statistical significance was assessed using Student’s t-test, with p -values represented as follows: ns: not significant ( p > 0.05); ∗: p ≤ 0.05. Because the M+2 labeling of the acetyl group may arise from either oxidative decarboxylation of pyruvate or reductive carboxylation of citrate, these two indistinguishable sources are jointly annotated as M+2 (Pyr/Cit). Abbreviations: Pyr/Cit, pyruvate- or citrate-derived M+2 (indistinguishable by MRM transitions); Gly, Glycine; For, Formate; R5P, Ribose-5-phosphate. # in x-axis indicates isotopomers with the same number of labeled carbon atoms incorporated, but with different origin and final moiety.

Article Snippet: The U-87 MG human brain immortalized cell line (ATCC® HTB-14TM) (wild type) or the R132H (IDH1 mutant) were plated at a density of 1 million cells per T75 plate in 10 mL complete ATCC Eagle’s Minimum Essential Medium (EMEM) 30-2003 medium, with 5 replicates per condition.

Techniques: Incubation, Mutagenesis, Labeling, Derivative Assay

Journal: bioRxiv

Article Title: Multi-omics and spatial analysis of microgravity-grown glioblastoma organoids reveals superior modeling of advanced disease after long-term spaceflight

doi: 10.64898/2026.03.06.710192

Figure Lengend Snippet: ( A ) Stacked bar plots summarize the number of significantly DEGs identified by DESeq2 (Benjamini-Hochberg corrected p < 0.05) for four contrasts derived from a model including gravity condition (uG vs KSC), co-culture condition (U87 GBM with and without THP-1 monocytes), and their interaction. Bars show DEGs for (i) U87 (uG vs KSC), (ii) U87THP (uG vs KSC), (iii) uG (U87THP vs U87), and (iv) KSC (U87THP vs U87). Counts are partitioned into upregulated (positive log2FC; light red) and downregulated (negative log2FC; light blue) genes, with the number of DEGs shown. An adjacent UpSet plot displays intersections among DESeq2-identified DEGs. Vertical bars indicate the number of genes in each intersection, and filled dots denote the contrasts contributing to each intersection. ( B ) Volcano plot shows DESeq2 results for the gravity * co-culture interaction term from a DESeq2 model including gravity condition (uG vs KSC), co-culture composition (U87 GBM with and without THP-1 monocytes), and their interaction. Each point represents a gene, plotted by the interaction log2 fold-change (x-axis; difference in the microgravity effect between U87THP and U87) and -log10 adjusted p-value (y-axis; Benjamini-Hochberg corrected). Genes with p < 0.05 are highlighted as significant (red/blue by direction), while non-significant genes are shown in gray; shaded regions indicate the significance threshold. All significant interaction genes are labeled. ( C ) Dot plots show DESeq2 log2 fold-change (uG vs KSC) estimates for selected genes (FAM50A, PRSS35, EPHA7, LINC01705) in U87 GBM alone and GBM co-cultured with THP-1 monocytes. Points indicate the estimated log2FC for each contrast, and error bars represent ±1 standard error (lfcSE). Lines connecting the two contrasts are shown to emphasize differences in direction and magnitude of the microgravity response depending on immune context. A dashed horizontal line marks no change (log2FC = 0). ( D ) GSEA of U87 GBM differentially expressed genes (uG vs KSC) was performed using GBM meta-programs (MPs) . Enrichment plot is shown for MES_2. Running enrichment score (ES) is plotted across the ranked gene list (top), with tick marks indicating positions of MES_2 genes in the ranked list (middle), and the underlying ranking metric shown below (bottom). The annotated inset reports the normalized enrichment score (NES) and Benjamini-Hochberg corrected p-value for MES_2 MP.

Article Snippet: Human GBM U87 cells and human monocyte THP-1 cells were purchased from ATCC (#HTB-14 and #TIB-202).

Techniques: Derivative Assay, Co-Culture Assay, Labeling, Cell Culture

Journal: bioRxiv

Article Title: Multi-omics and spatial analysis of microgravity-grown glioblastoma organoids reveals superior modeling of advanced disease after long-term spaceflight

doi: 10.64898/2026.03.06.710192

Figure Lengend Snippet: ( A ) Volcano plots show DESeq2 statistics comparing microgravity-grown organoids to Kennedy Space Center (KSC) 1 g controls for U87 GBM alone ( A ) and GBM co-cultured with THP-1 monocytes ( B ). Each point represents a gene, plotted by log2 fold change (x-axis; microgravity vs control) and -log10 adjusted p-value (y-axis; Benjamini-Hochberg corrected). Genes meeting p < 0.05 are highlighted as significantly upregulated (red) or downregulated (blue); non-significant genes are shown in gray. Shaded regions indicate the significance threshold (P < 0.05; fold-change threshold set to 0), and the top 20 most significant differentially expressed genes in each comparison are labeled. ( C ) Bar plots show Gene Ontology (GO) over-representation analysis (ORA) of genes differentially expressed in microgravity-grown organoids relative to KSC 1 g controls. Results are shown separately for U87 GBM alone ( C ) and U87 GBM co-cultured with THP-1 monocytes ( D ), with downregulated (blue; left-extending bars) and upregulated (red; right-extending bars) gene sets displayed in separate panels. Bars represent fold enrichment for selected GO terms, and color intensity encodes statistical significance (-log10 adjusted p-value, Benjamini-Hochberg correction). GO terms were simplified to reduce redundancy, and a curated subset of biologically relevant terms is shown for clarity.

Article Snippet: Human GBM U87 cells and human monocyte THP-1 cells were purchased from ATCC (#HTB-14 and #TIB-202).

Techniques: Cell Culture, Control, Comparison, Labeling

Journal: bioRxiv

Article Title: Multi-omics and spatial analysis of microgravity-grown glioblastoma organoids reveals superior modeling of advanced disease after long-term spaceflight

doi: 10.64898/2026.03.06.710192

Figure Lengend Snippet: ( A ) Gene set enrichment analysis (GSEA) was performed using GBM meta-program (MP) gene sets and Wald test DESeq2 statistic for U87 organoids grown in microgravity relative to KSC 1 g controls. Enrichment plots are shown for MP_1_RP (ribosomal protein program), MP_5_Hypoxia (hypoxia response), and MP_15_Stress2 (stress response). In each panel, the running enrichment score (ES) is plotted across the ranked gene list (top), with tick marks indicating positions of MP genes in the ranked list (middle), and the underlying ranking metric shown below (bottom). The annotated inset reports the normalized enrichment score (NES) and Benjamini-Hochberg corrected p-value for each meta-program. ( B ) Heatmap shows leading-edge genes (i.e. core enrichment genes) from GSEA presented in ( A ). Rows correspond to leading-edge genes, and columns represent individual samples annotated by experimental condition (top bar). The main heatmap displays mean-centered and scaled variance-stabilized expression values from DESeq2. The adjacent heatmap (“LFC”) shows the corresponding DESeq2 log2 fold change (microgravity vs control) for each leading-edge gene, with color indicating effect direction and magnitude. (C) GSEA of GBM meta-programs (MPs) was performed as in ( A ), but using DESeq2-ranked statistics from U87 organoids co-cultured with THP-1 monocytes grown in microgravity relative to KSC 1 g controls. (D) GSEA was performed on U87 organoids co-cultured with THP-1 monocytes using MSigDB Hallmark gene sets, with genes ranked by the DESeq2 Wald test statistic. ( E ) Scatter plots summarize HOMER motif enrichment results, with motifs ordered by significance (x-axis, rank) and plotted by motif enrichment log p-value (y-axis; more significant motifs appear higher due to reversed y-scale). Known motif enrichment results are shown for downregulated genes in U87 GBM (left) and upregulated genes in U87 + THP-1 monocyte co-culture (right). Each point represents one annotated HOMER motif; motifs passing significance threshold (P < 0.01, shaded region) are highlighted, and select motifs are labeled. ( F ) Density plot of HOMER-called motif offsets relative to the transcription start site (TSS) across genes used for enrichment analysis in ( I ); the dashed vertical line marks the TSS (0 bp). ( G ) Sequences logos and enrichment statistics are shown for significantly enriched motifs, based on analysis shown in ( E ). Gene Ontology (GO) over-representation analysis (ORA) was performed on downregulated and upregulated genes in U87 ( H ) and U87 + THP-1 monocyte ( I ) organoids, respectively, whose regulatory regions contained at least one TEAD1/2 (in U87; panel H ) or Smad3 (U87+THP-1; panel I ) motif match. Enriched GO terms were simplified to reduce redundancy. Bar plots display selected Biological Process terms (top terms by significance), with bar length indicating fold enrichment and color encoding statistical significance (-log10 p-value, Benjamini-Hochberg corrected). ( J ) Schematic demonstrating likely mechanism by which microgravity impacts GBM phenotype. Under normal gravity or mechanical force, RhoA promotes F-actin polymerization, facilitating YAP/TAZ nuclear localization and interaction with TEAD transcription factors to drive mesenchymal (MES) gene expression. In microgravity conditions, reduced mechanical loading disrupts cytoskeletal tension, leading to inhibition of YAP/TAZ activation and decreased transcription of MES-associated genes.

Article Snippet: Human GBM U87 cells and human monocyte THP-1 cells were purchased from ATCC (#HTB-14 and #TIB-202).

Techniques: Expressing, Control, Cell Culture, Co-Culture Assay, Labeling, Gene Expression, Inhibition, Activation Assay

Journal: bioRxiv

Article Title: Multi-omics and spatial analysis of microgravity-grown glioblastoma organoids reveals superior modeling of advanced disease after long-term spaceflight

doi: 10.64898/2026.03.06.710192

Figure Lengend Snippet: ( A ) Uniform Manifold Approximation and Projection (UMAP) embedding of the scRNA-seq reference dataset combining U87 GBM cells and THP-1 monocytes. Cells are colored by cell type. ( B ) Heatmap of marker gene expression in the scRNA-seq reference dataset. Marker sets include myeloid/innate immune genes (e.g., TYROBP, PTPRC, FCER1G, AIF1, APOE) and mesenchymal-like GBM genes (e.g., ALDH1A3, SERPINE1, TNC, SPARC, LOXL2). Genes were selected as markers identified by Wilcoxon rank-sum test and combined into a curated, nonredundant list for visualization. ( C ) Scatterplot of cell-type weights inferred by robust cell type decomposition (RCTD). Each point represents one cell, plotted by its inferred THP-1 weight (x-axis) and U87 weight (y-axis) from the RCTD weights matrix. The dashed diagonal indicates equal weights (y = x). ( D ) Dot plots summarizing the fraction of cells expressing canonical monocyte markers (CD14, FCN1, CCR2, CSF1R, FCGR1A, FCGR3A, ITGAM, ITGB2, SPI1, IRF8, SIRPA, CLEC12A, BST1). Left: scRNA-seq reference (U87 + THP-1). Right: Xenium single-cell dataset.

Article Snippet: Human GBM U87 cells and human monocyte THP-1 cells were purchased from ATCC (#HTB-14 and #TIB-202).

Techniques: Marker, Gene Expression, Expressing, Single Cell